[Bioperl-l] Installing Bio::DB::BigWig ?

[Dan Bolser]

I finally found the solution to this install problem. The error
message 'recompile with -fPIC' isn't referring to the Perl code, but
rather the jkucsc code...

In the directory .../src/kent/src/inc I changed the file common.mk to
add the -fPIC option to the CFLAGS...

[me at box inc]$ diff common.mk~ common.mk
6c6
< CFLAGS=
---
> CFLAGS=-fPIC


I then went back to .../src/kent/src/lib and hit 'make clean && make'.
Finally, going back to cpan, and re-installing Bio::DB::BigWig,
everything worked.


Sorry for the confusion, but it's been a long time since I needed to
install anything 'manually' ;-)

Dan.

# fun for everyone!
irc://irc.perl.org/#gmod

#also good!
irc://irc.freenode.net/#bioperl


On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> Trying to run make in .../src/kent/src (also CC'ing BP)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
> On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
>> Hi,
>>
>> I'm having trouble installing Bio::DB::BigWig.
>>
>> I grabbed the jkucsc code as described here [1] and built it
>> successfully after setting 'export MACHTYPE=x86_64'.
>>
>> I then set 'export KENT_SRC=.../src/kent/src' and called:
>> cpan[1]> install Bio::DB::BigWig
>>
>> The error comes:
>> ...
>> lib/Bio/DB/BigFile.xs:320: warning: unused variable ‘i’
>> lib/Bio/DB/BigFile.xs: In function
>> ‘XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended’:
>> lib/Bio/DB/BigFile.xs:358: warning: comparison is always false due to
>> limited range of data type
>> lib/Bio/DB/BigFile.xs:358: warning: operation on ‘summary’ may be undefined
>> lib/Bio/DB/BigFile.xs:354: warning: unused variable ‘summaryList’
>> lib/Bio/DB/BigFile.xs: In function
>> ‘XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended’:
>> lib/Bio/DB/BigFile.xs:395: warning: comparison is always false due to
>> limited range of data type
>> lib/Bio/DB/BigFile.xs:395: warning: operation on ‘summary’ may be undefined
>> lib/Bio/DB/BigFile.xs:391: warning: unused variable ‘summaryList’
>> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_chromList’:
>> lib/Bio/DB/BigFile.xs:424: warning: operation on ‘RETVAL’ may be undefined
>> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedIntervalQuery’:
>> lib/Bio/DB/BigFile.xs:450: warning: operation on ‘list’ may be undefined
>> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o
>> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
>> .../src/kent/src/lib/x86_64/jkweb.a -lz
>> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
>> relocation R_X86_64_32S against `a local symbol' can not be used when
>> making a shared object; recompile with -fPIC
>> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
>> lib/Bio/DB/BigFile.o at
>> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>>  LDS/Bio-BigFile-1.03.tar.gz
>>  ./Build -- NOT OK
>> ...
>>
>>
>> I tried to 'recompile with -fPIC', but saw further errors about
>> missing symbols that I can't fix.
>>
>> Are there some specific applications of the jkucsc package that I
>> should build and install first?
>>
>>
>> Thanks for any help,
>> Dan.
>>
>>
>> [1] http://genome.ucsc.edu/admin/git.html
>>
>